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Newsletter No. 495
August 7, 2023

ACA News, IUCr Newsletter, IUCr Meetings List


JULY 2023 PUBLICATIONS BY MEMBERS OF THE GROUP

1: Il Ahn J, Zhang L, Ravishankar H, Fan L, Kirsch K, Zeng Y, Meng L, Park JE,
Yun HY, Ghirlando R, Ma B, Ball D, Ku B, Nussinov R, Schmit JD, Heinz WF, Kim
SJ, Karpova T, Wang YX, Lee KS. Architectural basis for cylindrical self-
assembly governing Plk4-mediated centriole duplication in human cells
. Commun
Biol. 2023 Jul 11;6(1):712. doi: 10.1038/s42003-023-05067-8. Erratum in: Commun
Biol. 2023 Jul 27;6(1):784. PMID: 37433832; PMCID: PMC10336005.

2: Levdansky Y, Raisch T, Deme JC, Pekovic F, Elmlund H, Lea SM, Valkov E.
Structure and assembly of the NOT10:11 module of the CCR4-NOT complex. Commun
Biol. 2023 Jul 17;6(1):739. doi: 10.1038/s42003-023-05122-4. PMID: 37460791;
PMCID: PMC10352241.

3: Maiti A, Buffalo CZ, Saurabh S, Montecinos-Franjola F, Hachey JS, Conlon WJ,
Tran GN, Hassan B,
Walters KJ, Drobizhev M, Moerner WE, Ghosh P, Matsuo H, Tsien
RY, Lin JY, Rodriguez EA. Structural and photophysical characterization of the
small ultra-red fluorescent protein
. Nat Commun. 2023 Jul 12;14(1):4155. doi:
10.1038/s41467-023-39776-9. PMID: 37438348; PMCID: PMC10338489.

4: Zhong A, Jiang X, Hickman AB, Klier K, Teodoro GIC, Dyda F, Laub MT, Storz G.
Toxic antiphage defense proteins inhibited by intragenic antitoxin proteins.
Proc Natl Acad Sci U S A. 2023 Aug;120(31):e2307382120. doi:
10.1073/pnas.2307382120. Epub 2023 Jul 24. PMID: 37487082.

5: Kouno T, Shibata S, Shigematsu M, Hyun J, Kim TG,
Matsuo H, Wolf M.
Structural insights into RNA bridging between HIV-1 Vif and antiviral factor
APOBEC3G
. Nat Commun. 2023 Jul 7;14(1):4037. doi: 10.1038/s41467-023-39796-5.
PMID: 37419875; PMCID: PMC10328928.

6: Warden MS, DeRose EF, Tamayo JV, Mueller GA, Gavis ER, Hall TMT. The
translational repressor Glorund uses interchangeable RNA recognition domains to
recognize Drosophila nanos
. Nucleic Acids Res. 2023 Jul 10:gkad586. doi:
10.1093/nar/gkad586. Epub ahead of print. PMID: 37427795.

7: Holt GT, Gorman J, Wang S, Lowegard AU, Zhang B, Liu T, Lin BC, Louder MK,
Frenkel MS, McKee K, O'Dell S, Rawi R, Shen CH, Doria-Rose NA,
Kwong PD, Donald
BR. Improved HIV-1 neutralization breadth and potency of V2-apex antibodies by
in silico design
. Cell Rep. 2023 Jul 25;42(7):112711. doi:
10.1016/j.celrep.2023.112711. Epub 2023 Jul 11. PMID: 37436900.

8: Lannes L, Furman CM, Hickman AB,
Dyda F. Zinc-finger BED domains drive the
formation of the active Hermes transpososome by asymmetric DNA binding
. Nat
Commun. 2023 Jul 25;14(1):4470. doi: 10.1038/s41467-023-40210-3. PMID: 37491363;
PMCID: PMC10368747.

9: Wang S, Matassoli F, Zhang B, Liu T, Shen CH, Bylund T, Johnston T, Henry AR,
Teng IT, Tripathi P, Becker JE, Changela A, Chaudhary R, Cheng C, Gaudinski M,
Gorman J, Harris DR, Lee M, Morano NC, Novik L, O'Dell S, Olia AS, Parchment DK,
Rawi R, Roberts-Torres J, Stephens T, Tsybovsky Y, Wang D, Van Wazer DJ, Zhou T,
Doria-Rose NA, Koup RA, Shapiro L, Douek DC, McDermott AB,
Kwong PD. HIV-1
neutralizing antibodies elicited in humans by a prefusion-stabilized envelope
trimer form a reproducible class targeting fusion peptide
. Cell Rep. 2023 Jul
25;42(7):112755. doi: 10.1016/j.celrep.2023.112755. Epub 2023 Jul 11. PMID:
37436899.

For timely listing, please send a heads-up E-mail to the Editor upon publication.
METHODS - Room Temperature Biological Crystallography

 R.E. Thorne, "Determining biomolecular structures near room temperature using X-ray crystallography: conceptes, methods and future optimization"

 R.A. Steiner, "Introduction to the virtual thematic issue on room-temperature biological crystallography"

ARCHIVE: X-ray CrystallographyCryo-Electron MicroscopyIntegrative Structure Determination.

DISCUSSIONS - Name Change of the X-ray Diffraction SIG

F. Dyda, X. Ji: Considering rapid advancement of structural biology methods, we are proposing a change of the SIG name from "X-ray Diffraction" to "Structural Biology Methods," specifying that the SIG is mainly focused on methods in structural biology. Doing so, our SIG would be listed immediately after the "Structural Biology Interest Group" in the list of NIH SIGs. Please advise with your suggestions.

ARCHIVE: X-ray Crystallography, Protein Data Bank & Protein Folding.

READINGS AND TUTORIALS The Future of Structural Biology

R.J. Read et al., "AlphaFold and the future of structural biology" (2023)


ARCHIVE: CrystallographyX-ray DiffractionStructural BiologyStructure Prediction

 LINKS Suggestions?

Databases: DisProt, ExPASy, HAD, HIC-Up, NDBPDB, PDBe
, Protein Geometry
                  SARS-CoV-2 Related Structures, PDB SARS-CoV-2 Resources, AlphaFold DB,
                  virusMED, BioCyc, RaMP-DB,


Programs: CCP4, COOT, DSSR, HKLPHENIX, PyMOL, SOLVE, XDS


Servers: ACHESYM,
Anisotropy, C6@C3, DaliESPript, Grade, PDBePISA, Phyre2,
             MolProbity, RestraintLib, Robetta (RoseTTAFold),

Copyright © NIH X-Ray Diffraction Interest Group                       Maintained by Dr. Xinhua Ji